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lib/Bio/MUST/Apps/Leel/OrgProcessor.pm  view on Meta::CPAN

package Bio::MUST::Apps::Leel::OrgProcessor;
# ABSTRACT: Internal class for leel tool
$Bio::MUST::Apps::Leel::OrgProcessor::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments -ENV;

use Carp;
use Path::Class qw(file);
use Tie::IxHash;

use Bio::MUST::Core;
use Bio::MUST::Core::Constants qw(:seqids);
use Bio::MUST::Drivers;
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::Ali::Temporary';
use aliased 'Bio::MUST::Core::IdMapper';

with 'Bio::MUST::Apps::Roles::OrgProcable';


has 'ali_proc' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Apps::Leel::AliProcessor',
    required => 1,
);


has 'protein_seqs' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Ali::Temporary',
    init_arg => undef,
    lazy     => 1,
    builder  => '_build_protein_seqs',
    handles  => [
        qw(abbr_id_for long_id_for)
    ],
);


has 'protein_seq_mapper' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::IdMapper',
    init_arg => undef,
    lazy     => 1,
    builder  => '_build_protein_seq_mapper',
    handles  => {
        accession_for => 'long_id_for',
    },
);


has $_ . '_seqs' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Ali',
    init_arg => undef,
    lazy     => 1,
    builder  => '_build_' . $_ . '_seqs',
) for qw(transcript aligned);